Bioinformatics

FABI News

News Archive

23 Sep 2024

Researchers spotlight global threats from <I>Phytophthora</I> at International Conference

Researchers spotlight global threats from Phytophthora at International Conference

Drs Trudy Paap and Tanay Bose participated in the 11^th Meeting of IUFRO Working Party 7.02.09: Phytophthora in Forests and Natural Ecosystems.

13 Sep 2024

GRP Pest and Disease Diagnostic Clinic participates in Grain SA’s Farmers’ Days

FABI attended four Grain SA organised Farmers' Days recently to educate farmers about the GRP pest and disease extensions and diagnostic clinic services.

12 Sep 2024

Renowned fungal geneticist joins FABI as an Extraordinary Professor

FABI welcomes the renown fungal geneticist, Prof Fleißner, who joins FABI as an extraordinary Professor.

11 Sep 2024

FABI hosts a gathering to consider environmental fungi affecting human and animal health

FABI researchers recently hosted a group of colleagues from around the world having a specific interest in fungi that potentially affect the health of animals and humans.

9 Sep 2024

Nineteen FABIans capped at the UP Spring Graduation

FABI is proud of the 19 graduates being capped at the University of Pretoria’s Spring Graduation Ceremony.

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FABI Events

30 September 08h30

Monday Morning Meeting

03 October 08h30

Student Seminars

07 October 08h30

Monday Morning Meeting

10 October 08h30

Student Seminars

FABI in a nutshell

Research Features

Archive

Eleven new Penicillium and Talaromyces species discovered in South African culture collections.

A new study reveals the presence of Mycotoxins in Eastern Cape maize in South Africa.

Eurotiales update: FABIans Prof. Cobus Visagie and Dr Neriman Yilmaz and their collaborators have published a review of recently described Eurotiales species, including the economically important Aspergillus, Penicillium, Paecilomyces and Talaromyces.

Da Vinci's Yeast: FABIans Prof. Cobus Visagie, Dr Neriman Yilmaz, and their collaborators have recently described and named a newly discovered yeast species of the famous Italian painter, draughtsman, engineer, scientist, theorist, sculptor, and architect Leonardo da Vinci.

The potential economic impact of the PSHB invasion in South Africa has been calculated to be a massive R275 billion over the next ten years, if nothing is done to stop the spread of this invasive beetle. Researchers from FABI collaborated with Stellenbosch University ecologists and economists to model the unmitigated economic impact of this invasion.

A recently published paper in the journal Current Forestry Reports documents a collaboration between an international team of forest pathologists and invasion scientists. Led by Dr Trudy Paap, the authors present a framework for conceptualizing and managing invasive forest pathogens.

A recently published review article by Dr Andi Wilson in a special issue of the journal 'Microbiology & Molecular Biology Reviews' provides details of the genes that are essential to the sexual cycle in filamentous Ascomycete fungi and further describes their functions in a variety of model and non-model species.

Penicillium section Canescentia re-evaluated and five new species described from the fynbos biome in South Africa.

In November 2019, the DSI-NRF Centre of Excellence for Invasion Biology hosted a workshop on ‘Frameworks used in Invasion Science’. The workshop led to a NeoBiota special issue on this theme, and includes a review by FABI researchers and international colleagues, exploring frameworks in the context of forest pathology.

A doctoral study in FABI confirms for the first time the presence of Xylosandrus crassiusculus, a polyphagous ambrosia beetle and its fungal symbiont, Ambroseilla roeperi, in three provinces in South Africa. The authors warn that this beetle species could be a threat to native and plantation trees.

A review on invasive gall-forming wasps that threaten non-native Eucalyptus plantations by researchers in the TPCP appears in Agricultural and Forest Entomology. They profile several species of likely Australian origin that have established on non-native Eucalyptus plantations globally and discuss various challenges to their management.

A study in the TPCP confirms the identity of seven novel fungal species associated with Dendroctonus valens, the red turpentine beetle. The study follows on surveys on the fungal associates of the beetle in China and North America. Results from this work appear in Persoonia.

A postdoctoral study in the TPCP describes two novel Huntiella species in the African clade, bringing the number of known species in the genus to 31. Though closely related, the two species display different mating systems. Outcomes from this study appear in the journal MycoKeys.

A review of the invasion history and global management strategies of Eucalyptus snout beetles in the Gonipterus scutellatus species complex by researchers in the TPCP appears in the Journal of Pest Science.

In a collaborative venture with Dr Jos Houbraken (Westerdijk Fungal Biodiversity Institute, the Netherlands), Prof. Cobus M Visagie, Dr Neriman Yilmaz (both from FABI) and others have recently completed and published a major study updating the taxonomy of the Eurotiales.

A study in the Forest Molecular Genetics (FMG) Programme at FABI interrogates the benefits of implementing genomic selection for growth and wood quality traits in an established Eucalyptus grandis breeding programme in South Africa. Outcomes from this study appear in an article.

The first study on alternative weed and cultivated hosts of Spongospora subterraneaf. sp. subterranea (Sss), in southern Africa identifies two species as ideal trap crops for rotation with potatoes. The study also introduces three new families to the known hosts of Sss in the region.

A consortium of microbiologists from around the globe, FABI included, is pushing for an overhaul in how scientific names are assigned to uncultivated bacteria and archaea. Despite their ecological, agricultural and medical importance, these organisms traditionally have not been recognized by the international body governing the nomenclature of prokaryotes.

Professor Cobus Visagie is a researcher in the Applied Mycology group at FABI. One of the group’s research goals is to discover fungal diversity in South Africa, and Cobus’ research is strongly focussed on the economically important genera Aspergillus, Penicillium and Talaromyces.

Postdoctoral research by Dr Norman Muzhinji in the Potato Pathology Programme at the Forestry and Agricultural Biotechnology Institute (FABI) sheds light on the genetic structure and diversity of Spongospora subterranea f. sp. subterranea in four potato-growing regions in South Africa, providing valuable insights on its management.

An MSc study by Kira Lynn in the RGE-FABI Tree Health Programme at the University of Pretoria has described a new Fusarium species, Fusarium rekanum sp. nov., associated with Euwallacea perbrevis, an ambrosia beetle species infesting Acacia crassicarpa plantations in Riau, Indonesia.

FABI postdoctoral Fellow Dr Andi Wilson has established a CRISPR-Cas9-based genome editing protocol for use in Huntiella omanensis, a tree-inhabiting fungus belonging to the Ceratocystidaceae family.

Research undertaken as part of a PhD study by Molly Malefo at the University of Pretoria’s Department of Plant and Soil Sciences and Forestry and Agricultural Biotechnology Institute sheds more light on the role of protease inhibitors in plants under drought stress.

The South African National Biodiversity Institute (SANBI) has funded a postdoctoral research project dedicated to monitoring plant health in botanical gardens and arboreta across South Africa. Two postdoctoral Fellows at the University of Pretoria’s Forestry and Agricultural Biotechnology Institute have held these fellowships.

The first comprehensive study mapping the distribution and genetic diversity of invasive Eucalyptus insect pests in sub-Saharan Africa confirms the presence of five major foliage-feeding species in 14 countries. The results of this study have implications on the quarantine, future research and management of these pests on the continent and beyond.

Dr Joey Hulbert broke new ground when he became the first candidate at the Forestry and Agricultural Biotechnology Institute to complete a PhD study incorporating citizen science. Citizen science is an approach that involves members of the public as active participants in scientific research.

FABI technology unravels the genetics behind fungal genome evolution The RIPper is a bioinformatics tool for the for quantifying genome-wide RIP mutations in fungal genomes. The strength of this software lies in the automation of laborious techniques to study the mutation process called Repeat-Induced Point mutations (RIP). The RIPper applies these technique

With the increased availability in genome data, inferences regarding evolutionary relationships among taxa can now be performed on a genome-wide scale. But it is widely accepted that not all parts of such massive datasets support the same evolutionary hypothesis. Because of this, a group of researchers at FABI recently investigated the effect of this.

The use of genome data to characterize species and elucidate relationships, particularly between problematic taxa, has become routine practice in bacteria. Recently, researchers from FABI joined in an international effort to describe two novel genera and characterize these within the larger context of the important bacterial group Burkholderia.

A PhD student in FABI, Runlei Chang, has discovered and described 19 new fungal species from China as part of the research for his thesis. These fungi are all associated with conifer-infesting bark beetles and their mites and belong to well-known genera such as Ophiostoma and Leptographium.

Two research papers from FABI were selected as cover stories in two consecutive issues of the international journal, Plant Pathology. The journal is published by Wiley for the British Society of Plant Pathology.

Plastids play an integral role in wood formation, and yet they are routinely ignored in the study of xylogenesis in forest trees. Desre Pinard and Dr Eshchar Mizrachi have published a review highlighting the unique biology of plastids in wood, suggesting that a new type of plastid, the xylopast, exists.

Approaches for characterizing metabolic potential from genomic sequences have previously been predicted to be useful in the description of bacterial taxa. Dr Marike Palmer, has recently employed these approaches for identifying biological processes contributing to the divergence of bacteria with a variety of lifestyles.

Comparative genomics is shaping our notion of what fungal species are. Based on current data, these unique evolutionary units are separated from one another by boundaries that are porous under certain conditions. This affects our expectations regarding their population biology and evolution, and our strategies for recognizing and controlling them.

The Polyphagous Shot Hole Borer is an ambrosia beetle native to Southeast Asia. In 2017 this pest was detected in South Africa. Its presence has since been confirmed in all provinces except Limpopo. The beetle has a symbiotic relationship with the fungus Fusarium euwallaceae, which causes branch die-back and death of susceptible trees.

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The FMG Bioinformatics Platform is hosted in the Centre for Bioinformatics and Computational Biology at the University of Pretoria. Our team consists of a MIT big data science MSc student, Mr Christopher Marais, and a postdoctoral fellow, Dr Nanette Christie.

Working alongside biologists and geneticists in the FMG Programme, we are able to support and build capacity for the analysis, management and interpretation of large amounts of genomics and transcriptomics data for hundreds to thousands of individual trees. Web services, novel and commercial software, as well as a Galaxy workflow environment have been implemented to facilitate modular development of data processing and visualisation pipelines. These pipelines can be accessed remotely by group members for high-throughput genomics analysis and enable quality control, processing of raw data and downstream analyses such as gene and genome annotation, gene expression analysis, detection of genomic variants, and discovery of genetics associations with phenotypic traits.

We worked with colleagues at the Umea Plant Science Centre in Sweden on the integration of the Eucalyptus Genome Integrative Explorer (EucGenIE) into PlantGenIE (plantgenie.org), a dedicated web portal for genome and transcriptome exploration in plants (also including poplar, Norway spruce, and Arabidopsis). We also developed a web resource to query and visualise Eucalyptus systems genetics data, such as expression quantitative trait locus (eQTL) networks. We envision our genetic variation tool (qtlXplorer) to be a significant building block towards a population genomics module in PlantGenIE.

We are also hosting a genomic breeding database (BioPlasm) providing data access and analysis tools for tree breeders of our industry partners.

Workshops & Symposia

Archive

Workshop On The Biophysics Of Fungal Spore Dispersal

New Publications

Lin L, Fan XL, Groenewald JZ, Jami F, Wingfield MJ, Voglmayer H, Jaklitsch W, Castlebury LA, Tian CM, Crous PW. (2024) Cytospora: an important genus of canker pathogens. Studies in Mycology 109:323-401.

Cortina-Escribano M, Veteli P, Wingfield MJ, Wingfield BD, Coetzee MPA, Vanhanen H, Linnakoski R. (2024) Phylogenetic analysis and morphological characteristics of lactate Ganoderma specimens in Finland. Mycologia 10.1080/00275514.2024.2381424

van der Nest MA, Steenkamp ET, De Vos L, Wienk R, Swart V, van den Berg N. (2024) Complete mitochondrial genome sequence of the white root rot pathogen Dematophora necatrix (Xylariaceae: Xylariales). Mitochondrial DNA Part B: Resoures 9(9):1207-1212. 10.1080/23802359.2024.2403411

Nkomo T, Bose T, Wingfield BD, Knoppersen R, Mbhele O, Nemesio‐Gorriz M, Rodas CA, Paetz C, Cilliers CT, Ferreira MA, Hammerbacher A. (2024) Geographic location shapes fungal communities associated with Epidendrum roots. Mycological Progress 23:54. 10.1007/s11557-024-01990-0

Visagie CM, Houbraken J, Yilmaz N. (2024) The re-identification of Penicillium and Talaromyces (Eurotiales) catalogued in South African culture collections. Persoonia 53:29–61. 10.3767/persoonia.2024.53.02

Maduke N, Slippers B, Van der Linde E, Wingfield M, Fourie G. (2024) Botryosphaeriaceae species associated with branch dieback and decline of macadamia trees in South Africa. Australasian Plant Pathology :1-16. 10.1007/s13313-024-00992-6

Ribeiro MF, Cavallini G, Solce GN, Favoreto AL, Passos JRDS, Hurley BP, Wilcken CF. (2024) Polyandry contributes to Gonipterus platensis (Coleoptera: Curculionidae) rearing. PeerJ 12:e17929. 10.7717/peerj.17929

Basson RJ, Roets F, Wingfield MJ, Aylward J. (2024) Bark beetles and their associated fungi infesting native Widdringtonia species in the Western Cape province of South Africa. African Entomology 32(e18505) 10.17159/2254-8854/2024/a18505

van Heerden A, Pham NQ, Wingfield BD, Wingfield MJ, Wilken PM. (2024) Six type-I PKS classes and highly conserved melanin and elsinochrome gene clusters found in diverse Elsinoë species. Research Square 10.21203/rs.3.rs-4788746/v1

Solís M, Naidoo S, Wingfield MJ, Joubert J, Hammerbacher A. (2024) First line of defence: Eucalyptus leaf waxes influence infection by an aggressive fungal leaf pathogen. Plant Biology 10.1111/plb.13707

Nsibo DL, Barnes I, Berger DK. (2024) Recent advances in the population biology and management of maize foliar fungal pathogens Exserohilum turcicum, Cercospora zeina and Bipolaris maydis in Africa. Frontiers in Plant Science 15:1-23. https://doi.org/10.3389/fpls.2024.1404483

Lynn KMT, Wingfield MJ, Hammerbacher A, Barnes I. (2024) High-resolution melting curve analysis: A detection assay for Ceratocystis eucalypticola and C. manginecans in infected Eucalyptus. Fungal Biology 10.1016/j.funbio.2024.07.011

Yurkov A, Visagie CM, Crous PW, Hashimoto A, Baschien C, Begerow D, Kemler M, Schoutteten N, Stadler M, Wijayawardene NN, Hyde KD, Zhang N, Boekhout T, Group IYW, May TW, Thines M, Hawksworth DL. (2024) Cultures as types and the utility of viable specimens for fungal nomenclature. IMA Fungus 15:20. 10.1186/s43008-024-00155-8

Twiddy D, Fouché A, Akinsanmi OA, Fourie G. (2024) Biology and pathogenicity of fungi causing husk rot of macadamia in South Africa. European Journal of Plant Pathology :1-18. 10.1007/s10658-024-02915-z

Liu QL, Wingfield MJ, Duong TA, Wingfield BD, Chen SF. (2024) Diversity of Calonectria species from leaves and soils in diseased southern China Eucalyptus plantation. Fungal Biology 128:2007-2021. 10.1016/j.funbio.2024.07.007

Visagie CM, Yilmaz N, Allison JD, Barreto RW, Boekhout T, Boers J, Delgado MA, Dewing C, Fitza KNE, Furtado ECA, Gaya E, Hill R, Hobden A, Hu DM, Hülsewig T, Khonsanit A, Luangsa-Ard JJ, Mthembu A, Pereira CM, Price J-L, Pringle A, Qikani N, Sandoval-Denis M, Shumacher RK, Seifert KA, Slippers B, Tennakoon DS, Thanakitpipattana D, vanVuuren N, Groenewald JZ, Crous PW. (2024) New and Interesting Fungi. 7.. Fungal Systematics and Evolution 13:441–494. 10.3114/fuse.2024.13.12

Bhunjun C, Chen Y, Phukhamsakda C, Boekhout T, Groenewald J, McKenzie E, Francisco E, Frisvad J, Groenewald M, Hurdeal V, Luangsa-ard J, Perrone G, Visagie C, Bai F, Błaszkowski J, Braun U, D Souza F, De Q, Dutta A, Gonkhom D, Goto B, Guarnaccia V, Hagen F, Houbraken J, Lachance M, Li J, Luo K, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe D, Wang D, Wei D, Zhao C, Aiphuk W, Ajayi-Oyetunde O, Arantes T, Araujo J, Begerow D, Bakhshi M, Barbosa R, Behrens F, Bensch K, Bezerra J, Bilański P, Bradley C, Bubner B, Burgess T, Buyck B, Čadež N, Cai L, Calaça F, Campbell L, Chaverri P, Chen Y, Chethana K, Coetzee B, Costa M, Chen Q, Custódio F, Dai Y, Damm U, De Azevedo-Santiago A, De Miccolis-Angelini R, Dijksterhuis J, Dissanayake A, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake A, Gené J, Gomdola D, Gomes A, Hausner G, He M, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena R, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin C, Liu J, Liu X, Loizides M, Luangharn T, Maharachchikumbura S, Makhathini Mkhwanazi G, Manawasinghe I, Marin-Felix Y, McTaggart A, Moreau P, Morozova O, Mostert L, Osiewacz H, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips A, Phonemany M, Promputtha I, Rathnayaka A, Rodrigues A, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe S, Scholler M, Scott P, Shivas R, Silar P, Souza-Motta C, Silva-Filho A, Spies C, Stchigel A, Sterflinger K, Summerbell R, Svetasheva T, Takamatsu S, Theelen B, Theodoro R, Thines M, Thongklang N, Torres R, Turchetti B, Van den Brule T, Wang X, Wartchow F, Welti S, Wijesinghe S, Wu F, Xu R, Yang Z, Yilmaz N, Yurkov A, Zhao L, Zhao R, Zhou N, Hyde K, Crous P. (2024) What are the 100 most cited fungal genera?. Studies in Mycology 108:1-411. 10.3114/sim.2024.108.01

Coutinho TA, Carstensen G, Venter SN, Chen SF, Tarigan M, Wingfield MJ. (2024) Bacterial community in apparently healthy and asymptomatic Eucalyptus trees and those with symptoms of bacterial wilt. Journal of Plant Pathology 10.1007/s42161-024-01697-x

van Vuuren N, Yilmaz N, Wingfield MJ, Visagie CM. (2024) Five novel Curvularia species (Pleosporaceae, Pleosporales) isolated from fairy circles in the Namib desert. Mycological Progress 23:39. 10.1007/s11557-024-01977-x

Visagie CM, Cruywagen EM, Duong TA. (2024) A new Paecilomyces from wooden utility poles in South Africa. Fungal Systematics and Evolution 13:163–181. 10.3114/fuse.2024.13.10

Aylward J, Wilson AM, Visagie CM, Spraker J, Barnes I, Buitendag C, Ceriani C, Del Mar Angel L, du Plessis D, Fuchs T, Gasser K, Krämer D, Li W, Munsamy K, Piso A, Price J-L, Sonnekus B, Thomas C, van der Nest A, van Dijk A, van Heerden A, van Vuuren N, Yilmaz N, Duong TA, van der Merwe NA, Wingfield MJ, Wingfield BD. (2024) IMA Genome – F19: A genome assembly and annotation guide to empower mycologists, including annotated draft genome sequences of Ceratocystis pirilliformis, Diaporthe australafricana, Fusarium ophioides, Paecilomyces lecythidis, and Sporothrix stenoceras. IMA Fungus 15(1):12. 10.1186/s43008-024-00142-z

Ceriani C, Wingfield MJ, Fru F, van Wyk S, Rodas C, Wingfield BD, Steenkamp ET. (2024) Clonality and limited population diversity of Fusarium circinatum in Colombia. Forest Pathology 54(3):e12864. 10.1111/efp.12864

Jami F, Duma S, Fourie G, Schoeman M. (2024) First report of Botrytis cinerea causing flower blight on macadamia in South Africa. Journal of Phytopathology 72:e13325.:1-4. 10.1111/jph.13325

Paap T, Balocchi F, Burgess TI, Bose T, Wingfield MJ. (2024) A diverse range of Phytophthora species from botanical gardens in South Africa, including the novel Clade 5 species, Phytophthora mammiformis sp. nov.. Fungal Systematics and Evolution 13:111-122. 10.3114/fuse.2024.13.05

Ramaswe JB, Steenkamp ET, De Vos L, Fru FF, Adegeye OO, Wingfield BD. (2024) Sex pheromone receptor Ste2 orchestrates chemotropic growth towards pine root extracts in the pitch canker pathogen Fusarium circinatum. Pathogens 13:425. 10.3390/pathogens13050425

Midgley KA, van den Berg N, Swart V. (2024) Identification of Phytophthora cinnamomi CRN effectors and their roles in manipulating cell death during Persea americana infection. BMC Genomics 25:435. 10.1186/s12864-024-10358-3

Marais I, Buitendag C, Duong TA, Crampton BG, Theron J, Kidanemarium D, Berger DK. (2024) Double-stranded RNA uptake for the control of the maize pathogen Cercospora zeina. Plant Pathology 73(6):1480-1490. 10.1111/ppa.13909

van Heerden A, Pham NQ, Wingfield BD, Wingfield MJ, Muro Abad JI, Durán A, Wilken PM. (2024) LAMP assay to detect Elsinoë necatrix; an important Eucalyptus shoot and leaf pathogen. Plant Disease 10.1094/PDIS-01-24-0086-RE

Silva GA, Oliveira MES, Rêgo GMS, Wingfield BD, Wingfield MJ, Ferreira MA. (2024) Chrysoporthe brasiliensis sp. nov. pathogenic to Melastomataceae in southeast Brazil. Fungal Biology 10.1016/j.funbio.2024.04.001

Fick A, Swart V, Bombarely A, van den Berg N. (2024) Comparative transcriptional analysis of Persea americana MYB, WRKY and AP2/ERF transcription factors following Phytophthora cinnamomi infection. Molecular Plant Pathology 25(4):e13453. 10.1111/mpp.13453

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